The Mueller report contains tantalising details of Trump campaign dealings with Russia and of the president’s possible attempts to obstruct justice. But much of it is blacked out. Nearly 40% of the pages in the document contain at least one redaction, totalling nearly 1,000 in all. In some parts, entire sections have disappeared.

The redactions fall into four categories. The largest is “harm to ongoing matters”. This refers to likely future trials, including that of Trump’s friend and ally Roger Stone, who is due in court in November.

The second-biggest category is “grand jury”: material that might be used in ongoing legal matters. Information has also been removed which could compromise FBI “investigative techniques”. The fourth category is “personal privacy”. It concerns individuals peripheral to the core investigation by the special counsel, Robert Mueller.

Trump’s attorney general, William Barr, will release a less-redacted version of the report to Congress. A close reading of the 448-page report made public offers clues as to what is missing, including remarks made by Trump about sensitive matters.

1. Russian interference in the 2016 election

The report gives a voluminous account of how Russian military intelligence hacked and released Democratic party emails, and how Moscow used social media to boost Trump and damage Hillary Clinton. The campaign was conducted by the Internet Research Agency (IRA), a troll factory in St Petersburg funded by the businessman Yevgeny Prigozhin.

Details of the IRA’s structure, history and growth since 2014 have been redacted. Also hidden are paragraphs concerning Prigozhin’s background and ties to Vladimir Putin.

Paragraphs have been blacked out here because of “harm to ongoing matters”. They appear to illuminate work done by “Twitter specialists” and pro-Trump rallies organised by the IRA. Mueller has indicted Prigozhin and others but there is little prospect they will ever appear in a US court.

Some of the most intriguing missing sections concern the GRU spy agency. Technical details have been redacted on the grounds they might reveal FBI methods. They encompass how the GRU researched Democratic websites, surreptitious payments made by Bitcoin, and the lease of computers in Arizona and US cities.

Redactions in the Mueller report. Photograph: Reuters Graphics

2. Campaign interactions with GRU and WikiLeaks

Mueller concluded that there was not enough evidence to establish a criminal-level conspiracy between Trump aides and Moscow. However, his report makes clear that Trump and those around him sought to use the Kremlin’s hacking and dumping to their advantage.

There are crucial deletions over how the GRU transmitted stolen emails to WikiLeaks. “[Julian] Assange has access to the internet from the Ecuadorian embassy in London, England,” the report says, with the rest of the sentence redacted. Also struck out is the name of a Clinton aide targeted by the GRU in July 2016, after Trump appealed to Russia to find Clinton’s “missing 30,000 emails”.

The most striking section is titled The Trump Campaign and the Dissemination of Hacked Materials. The campaign “showed interest” in the leaked emails, the report says. But deletions make it difficult to piece together who communicated directly with WikiLeaks, what information was passed up to Trump, and when the campaign became aware of Moscow’s espionage work.

Rick Gates, Trump’s deputy campaign manager, who cooperated with Mueller, describes Trump as “generally frustrated” that Clinton’s emails had not been discovered. Other parts of his evidence are redacted. Similarly Michael Cohen, Trump’s personal lawyer, recalls talking to Trump in Trump Tower in July 2016, after WikiLeaks released the first tranche of emails.

“Candidate Trump said something to the effect of …” the report says. Trump’s comment is redacted.

The campaign chairman Paul Manafort’s conversation with Trump on the same theme is blacked out. One imagines Trump was thrilled by the emails’ publication but his remarks are missing.

3. Contacts with Russians

The report says the FBI began investigating Russian interference after a tip-off in July 2016. Australia’s high commissioner in London, Alexander Downer, met George Papadopoulos, a Trump foreign policy aide. A Maltese professor, Joseph Mifsud, told Papadopoulos Moscow was sitting on hacked emails and had “dirt” on Clinton.

Mueller says Mifsud travelled regularly to Moscow and was in contact with a former member of the IRA. The name has been blacked out. So is the identity of another Mifsud contact linked to Russia’s ministry of defence.

The next section concerns Carter Page, another Trump aide who in summer 2016 travelled to Moscow and held talks with Kremlin officials. Lines are blacked out, including part of an email sent by Page to senior campaign figures concerning policy on Russia. The redactions are explained as “grand jury”. Page has not been charged. It is unclear which case is meant here.

4. Prosecutions

This report looks at the conduct of individuals and whether they committed a federal offence. Mueller asks if there is enough evidence to sustain a conviction. He makes clear the criminal threshold is beyond reasonable doubt and does not include collusion, which is not a “term” under US law.

The special counsel refers to “two sets of charges” brought against Russians, GRU officers and IRA employees indicted in 2018. But the names of some Americans are hidden. One name buried is almost certainly that of Stone. A paragraph begins ‘Questions over whether …” and then disappears. Two names are rubbed out from a list that also includes Cohen and Trump’s first national security adviser, Michael Flynn.

5. Violation of campaign finance laws

The report examines possible campaign finance violations and considers if Trump campaign officials should be designated Russian agents. Lobbyists for foreign governments are obliged to register with the Department of Justice. Failure to do so is a crime: one of several charges against Manafort over his pre-Trump work in Ukraine.

Mueller writes at length about the notorious Trump Tower meeting in which Manafort, Donald Trump Jr and Trump’s son-in-law, Jared Kushner, met in June 2016 with a Russian lawyer. He decided not to pursue a criminal prosecution because of the “high burden” of proving a “culpable mental state”. A second similar instance is discussed – and entirely deleted.

6. Trump’s conduct

There are fewer blackouts in the second volume, which deals with possible obstruction of justice. Mueller lays out Trump’s conduct towards witnesses, his anxiety over where the Russia investigation is heading, the firing of the FBI director, James Comey, and his interactions with key players including Flynn and Manafort. Trump’s behaviour towards a third person is considered. We don’t know who this is. It might be Stone – or someone else. The relevant passages are scrubbed.

7. Referrals

The report contains appendices. One is a list of dramatis personae. Names are given in alphabetical order, some removed. They include mystery surnames beginning with G or H, K and M, and a line of biography concerning Stone.

The last section describes investigations which the special counsel has handed over to the FBI and the justice department. Two of these legal “transfers” – numbers nine and 11 – are rubbed out, the words “investigation ongoing” underneath. There are 13 redacted “referrals” of cases which fall outside the scope of Mueller’s inquiry.

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